Multiple sequence alignment - TraesCS4D01G042200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G042200 chr4D 100.000 2743 0 0 1 2743 19689895 19687153 0.000000e+00 5066.0
1 TraesCS4D01G042200 chr4B 88.504 1531 76 36 4 1476 32261982 32260494 0.000000e+00 1760.0
2 TraesCS4D01G042200 chr4B 89.545 440 17 11 1503 1913 32260180 32259741 5.200000e-147 531.0
3 TraesCS4D01G042200 chr4A 92.239 902 49 11 1529 2410 581270570 581271470 0.000000e+00 1258.0
4 TraesCS4D01G042200 chr4A 84.541 1352 73 51 180 1471 581269207 581270482 0.000000e+00 1214.0
5 TraesCS4D01G042200 chr4A 87.123 365 38 8 2198 2558 581272068 581272427 3.290000e-109 405.0
6 TraesCS4D01G042200 chr4A 90.674 193 18 0 2547 2739 581273112 581273304 9.750000e-65 257.0
7 TraesCS4D01G042200 chr4A 84.541 207 23 9 1539 1739 616977492 616977289 2.150000e-46 196.0
8 TraesCS4D01G042200 chr4A 83.495 206 27 7 1539 1739 616961551 616961348 4.660000e-43 185.0
9 TraesCS4D01G042200 chr4A 86.923 130 16 1 32 161 581268931 581269059 7.920000e-31 145.0
10 TraesCS4D01G042200 chr5B 86.730 211 19 9 1535 1739 703306141 703306348 2.750000e-55 226.0
11 TraesCS4D01G042200 chr5B 86.473 207 19 9 1539 1739 703269015 703269218 4.600000e-53 219.0
12 TraesCS4D01G042200 chr5B 85.922 206 20 9 1539 1738 703291898 703292100 7.700000e-51 211.0
13 TraesCS4D01G042200 chr5D 85.437 206 23 6 1539 1739 550646700 550646903 9.960000e-50 207.0
14 TraesCS4D01G042200 chr5D 84.834 211 23 9 1535 1739 551024896 551025103 1.290000e-48 204.0
15 TraesCS4D01G042200 chr5D 89.394 66 7 0 2409 2474 324318732 324318797 1.750000e-12 84.2
16 TraesCS4D01G042200 chr2B 90.000 100 3 3 866 958 77796897 77796798 3.710000e-24 122.0
17 TraesCS4D01G042200 chr2B 90.000 100 3 3 866 958 77800728 77800629 3.710000e-24 122.0
18 TraesCS4D01G042200 chr2B 89.000 100 3 4 866 958 77847650 77847552 1.730000e-22 117.0
19 TraesCS4D01G042200 chr5A 87.273 55 7 0 2407 2461 108206171 108206225 2.280000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G042200 chr4D 19687153 19689895 2742 True 5066.0 5066 100.0000 1 2743 1 chr4D.!!$R1 2742
1 TraesCS4D01G042200 chr4B 32259741 32261982 2241 True 1145.5 1760 89.0245 4 1913 2 chr4B.!!$R1 1909
2 TraesCS4D01G042200 chr4A 581268931 581273304 4373 False 655.8 1258 88.3000 32 2739 5 chr4A.!!$F1 2707

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
66 70 0.040646 TTCTGGAAGGAGGGCTACGA 59.959 55.0 0.00 0.00 0.0 3.43 F
1489 1742 0.033504 CGGACTGGCGCCACTATAAT 59.966 55.0 29.03 6.65 0.0 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1532 2074 1.152984 CCTGAACACTGCACCCACA 60.153 57.895 0.00 0.00 0.00 4.17 R
2499 3891 0.178903 TACCCCTTGCAGAGGTCAGT 60.179 55.000 7.57 7.39 44.71 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 64 4.592997 ATTAGGTTTTCTGGAAGGAGGG 57.407 45.455 0.00 0.00 0.00 4.30
61 65 0.405973 AGGTTTTCTGGAAGGAGGGC 59.594 55.000 0.00 0.00 0.00 5.19
64 68 2.618302 GGTTTTCTGGAAGGAGGGCTAC 60.618 54.545 0.00 0.00 0.00 3.58
66 70 0.040646 TTCTGGAAGGAGGGCTACGA 59.959 55.000 0.00 0.00 0.00 3.43
78 82 2.084546 GGGCTACGATCAAAGCAAGTT 58.915 47.619 15.88 0.00 40.61 2.66
80 84 3.057526 GGGCTACGATCAAAGCAAGTTTT 60.058 43.478 15.88 0.00 40.61 2.43
252 405 9.411801 CTGTACGCATGAACATAAATCTAGTAT 57.588 33.333 0.00 0.00 0.00 2.12
289 455 1.904144 CATGCATGCAGTAAGTGTGC 58.096 50.000 26.69 0.00 41.59 4.57
336 502 2.365768 GACTGACCTCCCCTCCCC 60.366 72.222 0.00 0.00 0.00 4.81
337 503 2.876858 ACTGACCTCCCCTCCCCT 60.877 66.667 0.00 0.00 0.00 4.79
338 504 2.041405 CTGACCTCCCCTCCCCTC 60.041 72.222 0.00 0.00 0.00 4.30
339 505 3.695825 TGACCTCCCCTCCCCTCC 61.696 72.222 0.00 0.00 0.00 4.30
340 506 4.500826 GACCTCCCCTCCCCTCCC 62.501 77.778 0.00 0.00 0.00 4.30
440 629 1.153939 CCTCCGACAGACAGCGAAG 60.154 63.158 0.00 0.00 0.00 3.79
472 671 0.891904 CTCTAGCTAGCTCCCCGTCC 60.892 65.000 23.26 0.00 0.00 4.79
519 718 1.130777 TCCATTCCCATCGATCAGCA 58.869 50.000 0.00 0.00 0.00 4.41
520 719 1.202687 TCCATTCCCATCGATCAGCAC 60.203 52.381 0.00 0.00 0.00 4.40
556 755 3.423154 CACCGCTTTCCACGCTCC 61.423 66.667 0.00 0.00 0.00 4.70
593 792 1.454479 CCATTGCCCCTGCCAGTAG 60.454 63.158 0.00 0.00 36.33 2.57
594 793 1.304282 CATTGCCCCTGCCAGTAGT 59.696 57.895 0.00 0.00 36.33 2.73
595 794 0.546122 CATTGCCCCTGCCAGTAGTA 59.454 55.000 0.00 0.00 36.33 1.82
596 795 1.064758 CATTGCCCCTGCCAGTAGTAA 60.065 52.381 0.00 0.00 36.33 2.24
598 797 0.326927 TGCCCCTGCCAGTAGTAAAC 59.673 55.000 0.00 0.00 36.33 2.01
599 798 0.618981 GCCCCTGCCAGTAGTAAACT 59.381 55.000 0.00 0.00 39.81 2.66
600 799 1.835531 GCCCCTGCCAGTAGTAAACTA 59.164 52.381 0.00 0.00 35.76 2.24
601 800 2.158943 GCCCCTGCCAGTAGTAAACTAG 60.159 54.545 0.00 0.00 35.76 2.57
602 801 2.158943 CCCCTGCCAGTAGTAAACTAGC 60.159 54.545 0.00 0.00 42.51 3.42
603 802 2.158943 CCCTGCCAGTAGTAAACTAGCC 60.159 54.545 0.00 0.00 41.61 3.93
604 803 2.500098 CCTGCCAGTAGTAAACTAGCCA 59.500 50.000 0.00 0.00 41.61 4.75
674 873 5.279306 GGTTTCAACCCAAGTAAATTCCTCC 60.279 44.000 0.00 0.00 43.43 4.30
740 948 1.074090 TCCCCTTGGACTCACACCA 60.074 57.895 0.00 0.00 35.03 4.17
765 973 1.947013 CACTGCACTGCTTCCACAG 59.053 57.895 1.98 0.00 43.59 3.66
776 984 0.603569 CTTCCACAGTGGCTAGACGT 59.396 55.000 15.64 0.00 37.47 4.34
777 985 1.000955 CTTCCACAGTGGCTAGACGTT 59.999 52.381 15.64 0.00 37.47 3.99
778 986 0.317160 TCCACAGTGGCTAGACGTTG 59.683 55.000 15.64 0.00 37.47 4.10
814 1022 2.515057 GTGTGGCAACCCGTGTGA 60.515 61.111 0.00 0.00 0.00 3.58
918 1138 4.021925 ACCCAAGCCTCCACTCGC 62.022 66.667 0.00 0.00 0.00 5.03
921 1141 2.345244 CAAGCCTCCACTCGCACT 59.655 61.111 0.00 0.00 0.00 4.40
935 1158 2.580867 CACTCACGCGCTCCTAGC 60.581 66.667 5.73 0.00 38.02 3.42
959 1182 1.447489 CTTCCTCTGCTCCTGCACG 60.447 63.158 0.00 0.00 45.31 5.34
960 1183 2.849120 CTTCCTCTGCTCCTGCACGG 62.849 65.000 0.00 0.00 45.31 4.94
978 1201 3.322466 CCGCACCTCCCTTCCACT 61.322 66.667 0.00 0.00 0.00 4.00
979 1202 2.266055 CGCACCTCCCTTCCACTC 59.734 66.667 0.00 0.00 0.00 3.51
981 1204 2.972819 GCACCTCCCTTCCACTCCC 61.973 68.421 0.00 0.00 0.00 4.30
982 1205 1.538876 CACCTCCCTTCCACTCCCA 60.539 63.158 0.00 0.00 0.00 4.37
984 1207 1.229658 CCTCCCTTCCACTCCCACT 60.230 63.158 0.00 0.00 0.00 4.00
985 1208 0.842467 CCTCCCTTCCACTCCCACTT 60.842 60.000 0.00 0.00 0.00 3.16
986 1209 0.615850 CTCCCTTCCACTCCCACTTC 59.384 60.000 0.00 0.00 0.00 3.01
987 1210 0.840722 TCCCTTCCACTCCCACTTCC 60.841 60.000 0.00 0.00 0.00 3.46
988 1211 1.133809 CCCTTCCACTCCCACTTCCA 61.134 60.000 0.00 0.00 0.00 3.53
989 1212 0.771127 CCTTCCACTCCCACTTCCAA 59.229 55.000 0.00 0.00 0.00 3.53
990 1213 1.144913 CCTTCCACTCCCACTTCCAAA 59.855 52.381 0.00 0.00 0.00 3.28
991 1214 2.508526 CTTCCACTCCCACTTCCAAAG 58.491 52.381 0.00 0.00 0.00 2.77
992 1215 0.110486 TCCACTCCCACTTCCAAAGC 59.890 55.000 0.00 0.00 0.00 3.51
993 1216 0.178992 CCACTCCCACTTCCAAAGCA 60.179 55.000 0.00 0.00 0.00 3.91
994 1217 1.242076 CACTCCCACTTCCAAAGCAG 58.758 55.000 0.00 0.00 0.00 4.24
1054 1277 4.154347 CGCTGGTCCTCCTCTGCC 62.154 72.222 0.00 0.00 34.23 4.85
1193 1416 4.704103 TGAGTGCTCGCCCTCCCT 62.704 66.667 0.00 0.00 0.00 4.20
1194 1417 3.844090 GAGTGCTCGCCCTCCCTC 61.844 72.222 0.00 0.00 0.00 4.30
1321 1565 0.453793 CCCTCAGTAGAGCAGACGTG 59.546 60.000 0.00 0.00 40.68 4.49
1352 1596 2.431539 CAAGAGTACGTCGTGCACC 58.568 57.895 15.94 6.96 0.00 5.01
1488 1741 1.324740 ACGGACTGGCGCCACTATAA 61.325 55.000 29.03 2.56 0.00 0.98
1489 1742 0.033504 CGGACTGGCGCCACTATAAT 59.966 55.000 29.03 6.65 0.00 1.28
1491 1744 2.671351 CGGACTGGCGCCACTATAATAG 60.671 54.545 29.03 16.25 0.00 1.73
1498 1751 3.131396 GCGCCACTATAATAGCACTGTT 58.869 45.455 0.00 0.00 0.00 3.16
1499 1752 3.560068 GCGCCACTATAATAGCACTGTTT 59.440 43.478 0.00 0.00 0.00 2.83
1501 1754 5.050490 CGCCACTATAATAGCACTGTTTCT 58.950 41.667 0.00 0.00 0.00 2.52
1505 2041 7.423199 CCACTATAATAGCACTGTTTCTCGTA 58.577 38.462 0.00 0.00 0.00 3.43
1532 2074 7.480760 AACTTGTGGGCTGAAATAAATGTAT 57.519 32.000 0.00 0.00 0.00 2.29
1697 2239 1.220206 CTTCATCTGCAGCGTCCCT 59.780 57.895 9.47 0.00 0.00 4.20
1757 2299 0.312416 CATGATCCGTCTCTCCGTCC 59.688 60.000 0.00 0.00 0.00 4.79
1758 2300 0.106669 ATGATCCGTCTCTCCGTCCA 60.107 55.000 0.00 0.00 0.00 4.02
1759 2301 0.106669 TGATCCGTCTCTCCGTCCAT 60.107 55.000 0.00 0.00 0.00 3.41
1761 2303 1.167155 ATCCGTCTCTCCGTCCATCG 61.167 60.000 0.00 0.00 39.52 3.84
1954 2528 7.780008 TGTACGTGCTTTAATGCTTGTATAT 57.220 32.000 13.80 0.00 0.00 0.86
1985 2559 4.269183 TGAGTTGTTGTGTCCTTTGTGAT 58.731 39.130 0.00 0.00 0.00 3.06
2012 2586 7.229506 ACTCCTTCCATTTCTTTTTACTCTGTG 59.770 37.037 0.00 0.00 0.00 3.66
2166 2741 6.707440 TTTGGTAGTGTGAATGTTGACAAT 57.293 33.333 0.00 0.00 0.00 2.71
2260 3650 9.110502 GAGTAAAAACAGGAACCCTAATATCTG 57.889 37.037 0.00 0.00 29.64 2.90
2261 3651 8.832735 AGTAAAAACAGGAACCCTAATATCTGA 58.167 33.333 0.00 0.00 29.64 3.27
2282 3672 1.152567 ATCCGCTGAGAGGGAGAGG 60.153 63.158 1.47 0.00 35.40 3.69
2325 3715 2.632996 CGCCAAGGACCCTAATATCTCA 59.367 50.000 0.00 0.00 0.00 3.27
2336 3726 5.130975 ACCCTAATATCTCATGCAGACACAA 59.869 40.000 0.00 0.00 32.26 3.33
2395 3786 2.908015 GTGCTTCCGCCTATGGGA 59.092 61.111 0.00 0.00 34.43 4.37
2398 3789 0.179020 TGCTTCCGCCTATGGGATTG 60.179 55.000 0.00 0.00 32.58 2.67
2400 3791 1.884235 CTTCCGCCTATGGGATTGTC 58.116 55.000 0.00 0.00 32.58 3.18
2401 3792 0.472471 TTCCGCCTATGGGATTGTCC 59.528 55.000 0.00 0.00 32.58 4.02
2402 3793 1.301716 CCGCCTATGGGATTGTCCG 60.302 63.158 0.00 0.00 37.43 4.79
2403 3794 1.445942 CGCCTATGGGATTGTCCGT 59.554 57.895 0.00 0.00 37.43 4.69
2405 3796 0.468226 GCCTATGGGATTGTCCGTGA 59.532 55.000 0.00 0.00 37.43 4.35
2406 3797 1.134220 GCCTATGGGATTGTCCGTGAA 60.134 52.381 0.00 0.00 37.43 3.18
2436 3828 7.932120 AGTTCGTCGAAATCTATTAAGATGG 57.068 36.000 9.70 0.00 41.81 3.51
2454 3846 9.838339 TTAAGATGGGATCTAGTTTCAAAGATC 57.162 33.333 4.15 4.15 44.88 2.75
2462 3854 8.610896 GGATCTAGTTTCAAAGATCTCAATGTG 58.389 37.037 11.05 0.00 44.94 3.21
2464 3856 9.730705 ATCTAGTTTCAAAGATCTCAATGTGAA 57.269 29.630 0.00 0.00 0.00 3.18
2480 3872 4.909696 TGTGAAAAATCCAACACGTGAT 57.090 36.364 25.01 7.78 36.25 3.06
2481 3873 5.255710 TGTGAAAAATCCAACACGTGATT 57.744 34.783 25.01 8.56 36.25 2.57
2482 3874 5.655488 TGTGAAAAATCCAACACGTGATTT 58.345 33.333 25.01 14.45 41.63 2.17
2545 3937 7.368059 CACTTTAAAAGTAATTTCGCTCCCTT 58.632 34.615 0.00 0.00 40.46 3.95
2553 3945 1.946984 TTTCGCTCCCTTTCCCTCTA 58.053 50.000 0.00 0.00 0.00 2.43
2562 4650 4.706616 TCCCTTTCCCTCTATTTGGTAGT 58.293 43.478 0.00 0.00 0.00 2.73
2566 4654 6.559157 CCCTTTCCCTCTATTTGGTAGTAGAT 59.441 42.308 0.00 0.00 0.00 1.98
2574 4662 7.299246 TCTATTTGGTAGTAGATAGCCCAAC 57.701 40.000 0.00 0.00 35.04 3.77
2595 4683 4.957296 ACGCCTTCTCTCTCTAAAAACAA 58.043 39.130 0.00 0.00 0.00 2.83
2610 4698 1.704641 AACAAAAGGAGAGCCCAACC 58.295 50.000 0.00 0.00 37.41 3.77
2613 4701 0.560688 AAAAGGAGAGCCCAACCCAA 59.439 50.000 0.00 0.00 37.41 4.12
2614 4702 0.178961 AAAGGAGAGCCCAACCCAAC 60.179 55.000 0.00 0.00 37.41 3.77
2618 4706 3.365265 GAGCCCAACCCAACGCAG 61.365 66.667 0.00 0.00 0.00 5.18
2622 4710 2.040544 CCCAACCCAACGCAGCTAG 61.041 63.158 0.00 0.00 0.00 3.42
2636 4724 2.498078 GCAGCTAGGGTGTTCTCTACTT 59.502 50.000 0.00 0.00 33.19 2.24
2638 4726 3.511934 CAGCTAGGGTGTTCTCTACTTGT 59.488 47.826 0.00 0.00 0.00 3.16
2669 4757 2.745515 GGAACCCCTATATGTCGCTC 57.254 55.000 0.00 0.00 0.00 5.03
2681 4769 2.815211 TCGCTCGTTGCATCCAGC 60.815 61.111 4.47 4.47 43.06 4.85
2715 4803 3.728373 GGGTGATCCAACCGGGCT 61.728 66.667 6.32 0.00 41.52 5.19
2719 4807 2.220586 TGATCCAACCGGGCTGACA 61.221 57.895 6.32 1.74 36.21 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.303537 CTACTCCTTTTTGTAATGCTAGTACTC 57.696 37.037 0.00 0.00 0.00 2.59
1 2 7.764901 GCTACTCCTTTTTGTAATGCTAGTACT 59.235 37.037 0.00 0.00 0.00 2.73
2 3 7.548075 TGCTACTCCTTTTTGTAATGCTAGTAC 59.452 37.037 0.00 0.00 0.00 2.73
8 9 5.880054 TCTGCTACTCCTTTTTGTAATGC 57.120 39.130 0.00 0.00 0.00 3.56
60 64 5.928153 ACTAAAACTTGCTTTGATCGTAGC 58.072 37.500 10.94 10.94 37.89 3.58
61 65 8.240883 ACTACTAAAACTTGCTTTGATCGTAG 57.759 34.615 0.00 0.00 0.00 3.51
64 68 6.797033 CCAACTACTAAAACTTGCTTTGATCG 59.203 38.462 0.00 0.00 0.00 3.69
66 70 6.447162 GCCAACTACTAAAACTTGCTTTGAT 58.553 36.000 0.00 0.00 0.00 2.57
78 82 3.367992 TCACGTTCGCCAACTACTAAA 57.632 42.857 0.00 0.00 0.00 1.85
80 84 2.488937 TCATCACGTTCGCCAACTACTA 59.511 45.455 0.00 0.00 0.00 1.82
252 405 6.709018 TGCATGCAGTTGAGTAGTATAGTA 57.291 37.500 18.46 0.00 0.00 1.82
253 406 5.598416 TGCATGCAGTTGAGTAGTATAGT 57.402 39.130 18.46 0.00 0.00 2.12
254 407 6.463483 CATGCATGCAGTTGAGTAGTATAG 57.537 41.667 26.69 0.00 0.00 1.31
289 455 1.736645 CAGGGTTGAGCGTACACGG 60.737 63.158 3.67 0.00 40.23 4.94
336 502 1.374252 CGGTGAGTTCAACCGGGAG 60.374 63.158 6.32 0.00 42.70 4.30
337 503 1.401318 TTCGGTGAGTTCAACCGGGA 61.401 55.000 14.41 0.00 46.03 5.14
338 504 0.321298 ATTCGGTGAGTTCAACCGGG 60.321 55.000 14.41 0.00 46.03 5.73
339 505 1.076332 GATTCGGTGAGTTCAACCGG 58.924 55.000 14.41 0.00 46.03 5.28
440 629 3.477224 CTAGAGGACGCCGAGCTGC 62.477 68.421 0.00 0.00 0.00 5.25
479 678 1.398799 AGGAGAAGGGAGAAGGGAGA 58.601 55.000 0.00 0.00 0.00 3.71
480 679 2.262266 AAGGAGAAGGGAGAAGGGAG 57.738 55.000 0.00 0.00 0.00 4.30
481 680 2.552367 GAAAGGAGAAGGGAGAAGGGA 58.448 52.381 0.00 0.00 0.00 4.20
482 681 1.562008 GGAAAGGAGAAGGGAGAAGGG 59.438 57.143 0.00 0.00 0.00 3.95
483 682 2.269940 TGGAAAGGAGAAGGGAGAAGG 58.730 52.381 0.00 0.00 0.00 3.46
484 683 4.522114 GAATGGAAAGGAGAAGGGAGAAG 58.478 47.826 0.00 0.00 0.00 2.85
485 684 3.267031 GGAATGGAAAGGAGAAGGGAGAA 59.733 47.826 0.00 0.00 0.00 2.87
519 718 1.595382 GTGAACGGTGCTGCTGAGT 60.595 57.895 0.00 0.00 0.00 3.41
520 719 1.287730 GAGTGAACGGTGCTGCTGAG 61.288 60.000 0.00 0.00 0.00 3.35
556 755 6.615088 CAATGGATTGTGAAGTTAGTCAAGG 58.385 40.000 0.00 0.00 33.22 3.61
593 792 4.017177 ACCTTTGGACTGGCTAGTTTAC 57.983 45.455 3.47 0.00 37.25 2.01
594 793 5.338871 CCATACCTTTGGACTGGCTAGTTTA 60.339 44.000 3.47 0.00 39.25 2.01
595 794 4.567747 CCATACCTTTGGACTGGCTAGTTT 60.568 45.833 3.47 0.00 39.25 2.66
596 795 3.054361 CCATACCTTTGGACTGGCTAGTT 60.054 47.826 3.47 0.00 39.25 2.24
598 797 2.746472 GCCATACCTTTGGACTGGCTAG 60.746 54.545 19.18 0.00 44.23 3.42
599 798 1.211949 GCCATACCTTTGGACTGGCTA 59.788 52.381 19.18 0.00 44.23 3.93
600 799 0.034089 GCCATACCTTTGGACTGGCT 60.034 55.000 19.18 0.00 44.23 4.75
601 800 1.037579 GGCCATACCTTTGGACTGGC 61.038 60.000 18.63 18.63 45.63 4.85
602 801 0.331278 TGGCCATACCTTTGGACTGG 59.669 55.000 0.00 0.00 45.84 4.00
603 802 1.463674 GTGGCCATACCTTTGGACTG 58.536 55.000 9.72 0.00 45.84 3.51
604 803 0.331616 GGTGGCCATACCTTTGGACT 59.668 55.000 9.72 0.00 45.84 3.85
674 873 0.464735 TGGGAAAGTTGGTGGTCGTG 60.465 55.000 0.00 0.00 0.00 4.35
755 963 0.321671 GTCTAGCCACTGTGGAAGCA 59.678 55.000 30.23 12.58 40.96 3.91
765 973 1.525619 GTGTGAACAACGTCTAGCCAC 59.474 52.381 0.00 0.00 0.00 5.01
771 979 2.867091 GCGCGTGTGAACAACGTCT 61.867 57.895 8.43 0.00 32.38 4.18
814 1022 3.869623 CCAAGAGTGTGGCTGCTAT 57.130 52.632 0.00 0.00 0.00 2.97
864 1072 0.108774 GCCTCCTTTTATAGCCGGCT 59.891 55.000 34.85 34.85 35.79 5.52
918 1138 2.580867 GCTAGGAGCGCGTGAGTG 60.581 66.667 8.43 0.00 46.39 3.51
921 1141 3.064987 GAAGGCTAGGAGCGCGTGA 62.065 63.158 8.43 0.00 43.62 4.35
927 1147 1.138069 GAGGAAGTGAAGGCTAGGAGC 59.862 57.143 0.00 0.00 41.46 4.70
935 1158 1.066286 CAGGAGCAGAGGAAGTGAAGG 60.066 57.143 0.00 0.00 0.00 3.46
963 1186 2.671682 GGAGTGGAAGGGAGGTGC 59.328 66.667 0.00 0.00 0.00 5.01
964 1187 1.538876 TGGGAGTGGAAGGGAGGTG 60.539 63.158 0.00 0.00 0.00 4.00
965 1188 1.539124 GTGGGAGTGGAAGGGAGGT 60.539 63.158 0.00 0.00 0.00 3.85
968 1191 0.840722 GGAAGTGGGAGTGGAAGGGA 60.841 60.000 0.00 0.00 0.00 4.20
969 1192 1.133809 TGGAAGTGGGAGTGGAAGGG 61.134 60.000 0.00 0.00 0.00 3.95
970 1193 0.771127 TTGGAAGTGGGAGTGGAAGG 59.229 55.000 0.00 0.00 0.00 3.46
971 1194 2.508526 CTTTGGAAGTGGGAGTGGAAG 58.491 52.381 0.00 0.00 0.00 3.46
972 1195 1.478654 GCTTTGGAAGTGGGAGTGGAA 60.479 52.381 0.00 0.00 0.00 3.53
974 1197 0.178992 TGCTTTGGAAGTGGGAGTGG 60.179 55.000 0.00 0.00 0.00 4.00
976 1199 0.846693 ACTGCTTTGGAAGTGGGAGT 59.153 50.000 0.00 0.00 28.33 3.85
978 1201 1.271379 GCTACTGCTTTGGAAGTGGGA 60.271 52.381 0.00 0.00 32.66 4.37
979 1202 1.168714 GCTACTGCTTTGGAAGTGGG 58.831 55.000 0.00 0.00 32.66 4.61
981 1204 1.795768 TCGCTACTGCTTTGGAAGTG 58.204 50.000 0.00 0.00 32.66 3.16
982 1205 2.350522 CATCGCTACTGCTTTGGAAGT 58.649 47.619 0.00 0.00 35.16 3.01
984 1207 1.737838 CCATCGCTACTGCTTTGGAA 58.262 50.000 0.00 0.00 39.63 3.53
985 1208 0.744414 GCCATCGCTACTGCTTTGGA 60.744 55.000 9.28 0.00 39.63 3.53
986 1209 0.745845 AGCCATCGCTACTGCTTTGG 60.746 55.000 0.00 0.00 46.08 3.28
987 1210 2.772739 AGCCATCGCTACTGCTTTG 58.227 52.632 0.00 0.00 46.08 2.77
999 1222 2.203126 CCGCTTCCCTGAGCCATC 60.203 66.667 0.00 0.00 39.51 3.51
1005 1228 4.704833 GCACTGCCGCTTCCCTGA 62.705 66.667 0.00 0.00 0.00 3.86
1054 1277 4.803426 GTCGCCGTGGAGGAGCAG 62.803 72.222 0.00 0.00 45.00 4.24
1108 1331 4.115199 GCTGAGGGCCCATCCGTT 62.115 66.667 27.56 0.00 34.94 4.44
1321 1565 2.175878 ACTCTTGCCACAGACATGTC 57.824 50.000 18.47 18.47 37.65 3.06
1446 1695 2.078914 CGTTTCCCGACTCGTCACG 61.079 63.158 0.00 0.00 39.56 4.35
1448 1697 2.049802 GCGTTTCCCGACTCGTCA 60.050 61.111 0.00 0.00 39.56 4.35
1473 1722 1.691976 TGCTATTATAGTGGCGCCAGT 59.308 47.619 37.19 37.19 0.00 4.00
1488 1741 6.512342 AGTTAGTACGAGAAACAGTGCTAT 57.488 37.500 0.00 0.00 35.94 2.97
1489 1742 5.954296 AGTTAGTACGAGAAACAGTGCTA 57.046 39.130 0.00 0.00 35.13 3.49
1491 1744 4.743644 ACAAGTTAGTACGAGAAACAGTGC 59.256 41.667 0.00 0.00 0.00 4.40
1498 1751 2.895404 AGCCCACAAGTTAGTACGAGAA 59.105 45.455 0.00 0.00 0.00 2.87
1499 1752 2.230508 CAGCCCACAAGTTAGTACGAGA 59.769 50.000 0.00 0.00 0.00 4.04
1501 1754 2.241160 TCAGCCCACAAGTTAGTACGA 58.759 47.619 0.00 0.00 0.00 3.43
1505 2041 6.493458 ACATTTATTTCAGCCCACAAGTTAGT 59.507 34.615 0.00 0.00 0.00 2.24
1532 2074 1.152984 CCTGAACACTGCACCCACA 60.153 57.895 0.00 0.00 0.00 4.17
1801 2354 3.821600 AGTAGCTTCAGTCACTCGAAGAA 59.178 43.478 16.66 0.00 40.94 2.52
1954 2528 5.652014 AGGACACAACAACTCAAAATTCTGA 59.348 36.000 0.00 0.00 0.00 3.27
1985 2559 8.437575 ACAGAGTAAAAAGAAATGGAAGGAGTA 58.562 33.333 0.00 0.00 0.00 2.59
2112 2687 9.223099 TGTCATTCGATGCATCATAGATTTAAT 57.777 29.630 25.70 8.95 0.00 1.40
2126 2701 4.675510 ACCAAATCAATGTCATTCGATGC 58.324 39.130 0.00 0.00 0.00 3.91
2260 3650 1.791103 CTCCCTCTCAGCGGATCGTC 61.791 65.000 0.00 0.00 0.00 4.20
2261 3651 1.826054 CTCCCTCTCAGCGGATCGT 60.826 63.158 0.00 0.00 0.00 3.73
2296 3686 1.003233 AGGGTCCTTGGCGAACTAAAG 59.997 52.381 0.00 0.00 0.00 1.85
2416 3808 7.316640 AGATCCCATCTTAATAGATTTCGACG 58.683 38.462 0.00 0.00 39.11 5.12
2430 3822 8.100135 AGATCTTTGAAACTAGATCCCATCTT 57.900 34.615 0.00 0.00 45.05 2.40
2432 3824 7.504403 TGAGATCTTTGAAACTAGATCCCATC 58.496 38.462 0.00 2.14 45.05 3.51
2436 3828 8.610896 CACATTGAGATCTTTGAAACTAGATCC 58.389 37.037 0.00 2.51 45.05 3.36
2454 3846 5.173673 CACGTGTTGGATTTTTCACATTGAG 59.826 40.000 7.58 0.00 0.00 3.02
2484 3876 7.519970 GCAGAGGTCAGTTCTAAATTCGAAAAA 60.520 37.037 0.00 0.00 0.00 1.94
2486 3878 5.408604 GCAGAGGTCAGTTCTAAATTCGAAA 59.591 40.000 0.00 0.00 0.00 3.46
2487 3879 4.929808 GCAGAGGTCAGTTCTAAATTCGAA 59.070 41.667 0.00 0.00 0.00 3.71
2490 3882 5.123027 CCTTGCAGAGGTCAGTTCTAAATTC 59.877 44.000 6.74 0.00 40.95 2.17
2494 3886 2.303022 CCCTTGCAGAGGTCAGTTCTAA 59.697 50.000 12.18 0.00 44.71 2.10
2497 3889 0.322008 CCCCTTGCAGAGGTCAGTTC 60.322 60.000 12.18 0.00 44.71 3.01
2499 3891 0.178903 TACCCCTTGCAGAGGTCAGT 60.179 55.000 7.57 7.39 44.71 3.41
2500 3892 0.250513 GTACCCCTTGCAGAGGTCAG 59.749 60.000 7.57 2.68 44.71 3.51
2505 3897 0.693049 AAGTGGTACCCCTTGCAGAG 59.307 55.000 9.03 0.00 0.00 3.35
2507 3899 2.871096 TAAAGTGGTACCCCTTGCAG 57.129 50.000 10.65 0.00 0.00 4.41
2521 3913 7.520451 AAGGGAGCGAAATTACTTTTAAAGT 57.480 32.000 14.99 14.99 45.40 2.66
2525 3917 5.416639 GGGAAAGGGAGCGAAATTACTTTTA 59.583 40.000 0.00 0.00 0.00 1.52
2538 3930 2.242452 ACCAAATAGAGGGAAAGGGAGC 59.758 50.000 0.00 0.00 0.00 4.70
2545 3937 6.724905 GGCTATCTACTACCAAATAGAGGGAA 59.275 42.308 0.00 0.00 34.65 3.97
2553 3945 4.742743 GCGTTGGGCTATCTACTACCAAAT 60.743 45.833 0.00 0.00 42.28 2.32
2574 4662 5.924475 TTTGTTTTTAGAGAGAGAAGGCG 57.076 39.130 0.00 0.00 0.00 5.52
2595 4683 0.178961 GTTGGGTTGGGCTCTCCTTT 60.179 55.000 0.00 0.00 36.20 3.11
2610 4698 1.298859 GAACACCCTAGCTGCGTTGG 61.299 60.000 0.00 0.00 0.00 3.77
2613 4701 0.900647 AGAGAACACCCTAGCTGCGT 60.901 55.000 0.00 0.00 0.00 5.24
2614 4702 1.103803 TAGAGAACACCCTAGCTGCG 58.896 55.000 0.00 0.00 0.00 5.18
2618 4706 3.368531 CCACAAGTAGAGAACACCCTAGC 60.369 52.174 0.00 0.00 0.00 3.42
2622 4710 1.071699 TGCCACAAGTAGAGAACACCC 59.928 52.381 0.00 0.00 0.00 4.61
2636 4724 0.755686 GGTTCCCATTGTTTGCCACA 59.244 50.000 0.00 0.00 0.00 4.17
2638 4726 1.124477 GGGGTTCCCATTGTTTGCCA 61.124 55.000 10.25 0.00 44.65 4.92
2681 4769 1.069765 CCTATGCACCCCGCTACTG 59.930 63.158 0.00 0.00 43.06 2.74
2715 4803 0.949397 CGGTAGCCGCTAGTATGTCA 59.051 55.000 0.00 0.00 41.17 3.58


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.